Leena Myllys

Monophyletic groups within the Parmeliaceae identified by ITS rDNA, beta-tubulin and GAPDH sequences

Phylogenetic relationships within the Parmeliaceae are analysed cladistically on the basis of DNA characters from partial β-tubulin, partial glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and ITS sequences. 100 taxa representing 73 of the 88 genera currently recognised are included in the analyses. Eight monophyletic groups including two or more genera were identified in the tree calculated from the combined data matrix. Three of the groups cover almost half of the species of the family. The largest and strongest supported group includes seven genera with their distribution centres in the Southern Hemisphere: Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Xanthomaculina and Xanthoparmelia. The second group is a clade of four essentially tropical genera: Concamerella, Flavoparmelia, Parmotrema and Rimelia. The third large group with strong support is the core of cetrarioid lichens, distributed primarily in cold areas of the Northern Hemisphere. The genus Parmelia sensu Hale is not closely related with most of its segregates. One new combination, Cetrariella commixta, is proposed. Coelopogon abraxas is reported from South America for the first time.

Phylogeny of cetrarioid lichens (Parmeliaceae) inferred from ITS and beta-tubulin sequences, morphology, anatomy and secondary chemistry.

Phylogenetic relationships within the family Parmeliaceae (lichenized ascomycetes) with emphasis on the heterogeneous group of cetrarioid lichens are reconstructed. The results are based on cladistic analyses of DNA-sequences, morphological and chemical data. Almost all currently recognized cetrarioid genera were included in the analyses together with parmelioid and alectorioid members of the presumably monophyletic family Parmeliaceae. We tried to sample taxonomic diversity of the family as widely as possible. The ITS1-5.8S-ITS2 region of the rDNA and a partial β-tubulin gene from 126 samples representing 82 species were analysed. Cetrarioid lichens were identified as a monophyletic group, supported by both ITS and β-tubulin characters. This group was reanalysed using 47 morphological, anatomical and secondary chemistry characters combined with the DNA data matrix. ITS and β-tubulin sequences provide congruent information, and a clear correlation between DNA-data and conidial shape is observed. The current taxonomy of the cetrarioid lichens is discussed and compared with the phylogenetic trees obtained here. A comprehensive study of the phylogeography of some bipolar or subcosmopolitic species with representatives from both hemispheres was performed. Cetraria aculeata is the only taxon where correlation between DNA-data and geographic origin is observed.

Multiple origins of symbioses between ascomycetes and bryophytes suggested by a five-gene phylogeny

Numerous species of microscopic fungi inhabit mosses and hepatics. They are severely overlooked and their identity and nutritional strategies are mostly unknown. Most of these bryosymbiotic fungi belong to the Ascomycota. Their fruit‐bodies are extremely small, often reduced and simply structured, which is why they cannot be reliably identified and classified by their morphological and anatomical characters. A phylogenetic hypothesis of bryosymbiotic ascomycetes is presented. New sequences of 78 samples, including 61 bryosymbionts, were produced, the total amount of terminals being 206. Of these, 202 are Ascomycetes. Sequences from the following five gene loci were used: rDNA SSU, rDNA LSU, RPB2, mitochondrial rDNA SSU, and rDNA 5.8S. The program TNT was used for tree search and support value estimation. We show that bryosymbiotic fungi occur in numerous lineages, one of which represents a newly discovered lineage among the Ascomycota and exhibits a tripartite association with cyanobacteria and sphagna. A new genus Trizodia is proposed for this basal clade. Our results demonstrate that even highly specialized life strategies can be adopted multiple times during evolution, and that in many cases bryosymbionts appear to have evolved from saprobic ancestors.

Evolution of complex symbiotic relationships in a morphologically derived family of lichen-forming fungi.

We studied the evolutionary history of the Parmeliaceae (Lecanoromycetes, Ascomycota), one of the largest families of lichen-forming fungi with complex and variable morphologies, also including several lichenicolous fungi. We assembled a six-locus data set including nuclear, mitochondrial and low-copy protein-coding genes from 293 operational taxonomic units (OTUs). The lichenicolous lifestyle originated independently three times in lichenized ancestors within Parmeliaceae, and a new generic name is introduced for one of these fungi. In all cases, the independent origins occurred c. 24 million yr ago. Further, we show that the Paleocene, Eocene and Oligocene were key periods when diversification of major lineages within Parmeliaceae occurred, with subsequent radiations occurring primarily during the Oligocene and Miocene. Our phylogenetic hypothesis supports the independent origin of lichenicolous fungi associated with climatic shifts at the Oligocene-Miocene boundary. Moreover, diversification bursts at different times may be crucial factors driving the diversification of Parmeliaceae. Additionally, our study provides novel insight into evolutionary relationships in this large and diverse family of lichen-forming ascomycetes.

Phylogeny of the cetrarioid core (Parmeliaceae) based on five genetic markers

Fourteen genera belong to a monophyletic core of cetrarioid lichens, Ahtiana, Allocetraria, Arctocetraria, Cetraria, Cetrariella, Cetreliopsis, Flavocetraria, Kaernefeltia, Masonhalea, Nephromopsis, Tuckermanella, Tuckermannopsis, Usnocetraria and Vulpicida. A total of 71 samples representing 65 species (of 90 worldwide) and all type species of the genera are included in phylogentic analyses based on a complete ITS matrix and incomplete sets of group I intron, β-tubulin, GAPDH and mtSSU sequences. Eleven of the species included in the study are analysed phylogenetically for the first time, and of the 178 sequences, 67 are newly constructed. Two phylogenetic trees, one based solely on the complete ITS-matrix and a second based on total information, are similar, but not entirely identical. About half of the species are gathered in a strongly supported clade composed of the genera Allocetraria, Cetraria s. str., Cetrariella and Vulpicida. Arctocetraria, Cetreliopsis, Kaernefeltia and Tuckermanella are monophyletic genera, whereas Cetraria, Flavocetraria and Tuckermannopsis are polyphyletic. The taxonomy in current use is compared with the phylogenetic results, and future, probable or potential adjustments to the phylogeny are discussed. The single non-DNA character with a strong correlation to phylogeny based on DNA-sequences is conidial shape. The secondary chemistry of the poorly known species Cetraria annae is analyzed for the first time; the cortex contains usnic acid and atranorin, whereas isonephrosterinic, nephrosterinic, lichesterinic, protolichesterinic and squamatic acids occur in the medulla. Notes on the anatomy of Cetraria annae and Flavocetraria minuscula are also provided.

Molecular data show that Bryoria fremontii and B. tortuosa (Parmeliaceae) are conspecific

Bryoria fremontii and B. tortuosa are the only species in the lichenized ascomycete genus Bryoria known to contain the pulvinic acid derivative vulpinic acid. In B. fremontii this yellow pigment is restricted to the soralia and apothecia, while in B. tortuosa it can occur throughout the thallus. The actual amount of vulpinic acid produced by B. tortuosa is rather variable, however, with intermediate specimens bearing both white and yellow pseudocyphellae. We studied the relationship between the two species with parsimony analysis using four DNA regions: 1) the internal transcribed spacers of the nuclear rDNA including the 5.8S region (ITS), 2) partial sequences from the intergenic spacer of the nuclear rDNA (IGS), 3) partial sequences from the small subunit of the mitochondrial rDNA (mtSSU), and 4) partial sequences from the protein-coding glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH). Our phylogenetic analysis revealed that B. fremontii and B. tortuosa must be regarded as conspecific, but allowing for some genetic differentiation between European and North American populations. Bryoria tortuosa is therefore synonymized with B. fremontii .

High selectivity in symbiotic associations of lichenized ascomycetes and cyanobacteria

The selectivity of mycobionts and cyanobionts in lichen symbioses were examined. We analyzed symbiotic cyanobionts, collected from different sample sites, and compared them to free‐living cyanobacteria Nostoc. Cyanobionts were obtained from lichens assigned to the genera Pseudocyphellaria and Sticta, in particular. Multiple gene loci were screened and direct optimization was used in the phylogenetic analyses. We show that many lichen fungi are strongly selective towards their cyanobionts. Lichenized ascomycetes seem to be able to identify and choose a specific strain, species or a species group of Nostoc with which to associate. The present analyses also suggest that some of the Nostoc taxa may be specialized in symbiotic life with only lichenized ascomycetes. Despite the selectivity observed in fungi, there appears to be no coevolution between the partners. We have also discussed the problems of using the tRNALeu intron as a marker in phylogenetic analyses.

Phylogenetic hypotheses: Cladoniaceae, Stereocaulaceae, Baeomycetaceae, and Icmadophilaceae revisited

Parsimony analyses of SSU rDNA sequences were conducted to examine phylogenetic relationships of selected genera within the families Cladoniaceae, Stereocaulaceae, Icmadophilaceae and Baeomycetaceae (lichen-forming ascomycetes). The analyses included 93 taxa (84 species) representing various groups of ascomycetous fungi. Analyses of the matrix with pre-aligned sequences were performed using heuristic and parsimony ratchet searches, and support values for the same matrix were calculated using parsimony jackknifing. The results support the recognition of the four families. Cladoniaceae are recircumscribed to accommodate Cladia, Cladonia, Heterodea, Metus, Pilophorus, Pycnothelia, Ramalea, Thysanothecium and the newly erected genus Carassea. Myelorrhiza is excluded from the family, while the status of other potential members, Calathaspis, Gymnoderma s.str. and Squamella, remains unresolved. Baeomycetaceae include Baeomyces and Phyllobaeis. Stereocaulaceae include Stereocaulon only, although the status of Muhria is still unclear. Finally, Icmadophilaceae include Dibaeis, Endocena, Knightiella, Icmadophila, Siphula and Thamnolia, while the status of Pseudobaeomyces and Siphulella requires further elucidation. The genus Cladonia appeared to be a polyphyletic assemblage, and accordingly, a new genus Carassea S. Stenroos, gen. nov., represented by C. connexa (Vain.) S. Stenroos, comb. nov., is described. Carassea is most closely related to Pycnothelia and Metus in the Cladoniaceae. Siphula, represented in the present analysis by six species, is not monophyletic, and is in need of reclassification.

Phylogeny of the genus Bryoria

The phylogenetic relationships of the genus Bryoria were examined using ITS, partial glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and mitochondrial SSU rDNA sequence data in addition to 20 chemical and morphological characters. This first comprehensive molecular study to assess Bryoria phylogeny includes representatives from all the traditionally recognized four sections. Combined cladistic analyses of 88 Bryoria specimens representing at least 25 species resulted in highly resolved phylogenies. Based on the results, a new infrageneric classification for the genus is proposed. Five sections are recognized, largely corresponding to the existing classification, with the addition of section Americanae. The study shows that while most species with an erect growth-form are clearly monophyletic, current species status of many pendent taxa can be questioned.

Cladistic analysis of Echinodorus (Alismataceae): simultaneous analysis of molecular and morphological data

Echinodorus is the second largest genus in the aquatic plant family Alismataceae. The genus is naturally distributed in the New World, but many species are known world‐wide as popular aquarium plants. The views upon species delimitation and infrageneric classification of the genus have been controversial. Phenotypic plasticity of aquatic plants combined with reduced and presumably convergent morphological structures pose serious problems to classification, emphasizing the need for molecular‐level data. A simultaneous cladistic analysis of molecular and morphological data was conducted to resolve the phylogeny of the genus. The results showed Echinodorus (as it is currently circumscribed) to be polyphyletic. None of the currently proposed infrageneric classifications of the genus were supported in the light of phylogenetic evidence. Also, many species and subspecies level rankings were found to be unnatural. Monophyly of Echinodorus is ascertained by separating Helanthium and the monotypic genus Albidella from Echinodorus. As a result, two new combinations (Helanthium bolivianum and H. zombiense) are made, and a detailed description of the genus Helanthium is provided.